Difference between revisions of "Talk:Fabry:Sequence-based mutation analysis"

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(Created page with "== Praise == * Nice tables * Nice visualizations of the mutated residues. Is this pymol? * Plenty of physicochemical properties. == Criticism == * Does the secondary structure…")
 
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== Criticism ==
 
== Criticism ==
 
* Does the secondary structure prediction refer to the sequence before or after the mutation?
 
* Does the secondary structure prediction refer to the sequence before or after the mutation?
  +
--> Since we used the files from Task 3 (see Journal), it is from the native structure
 
* What are your reasons for taking into account the substitution score of PAM1 and PAM250? Is the evolutionary distance not too short and too far, respectively?
 
* What are your reasons for taking into account the substitution score of PAM1 and PAM250? Is the evolutionary distance not too short and too far, respectively?
  +
--> We were said to do that
 
* I think the substitution scores of the three matrices are not directly comparable. PAM1 should have lower scores than PAM250 relative to the maximum score.
 
* I think the substitution scores of the three matrices are not directly comparable. PAM1 should have lower scores than PAM250 relative to the maximum score.
  +
--> We díd compare them relatively not the absolute values
 
* What do the entries in the PSSM table mean? It is obviously not the substitution score. In case of P40S: is P(P|40) = 0.81 or P(S|40) = 0.81?
 
* What do the entries in the PSSM table mean? It is obviously not the substitution score. In case of P40S: is P(P|40) = 0.81 or P(S|40) = 0.81?
 
* You classify the features either as disease causing or not disease causing. But what if a feature is in between?
 
* You classify the features either as disease causing or not disease causing. But what if a feature is in between?
  +
--> There are more severe forms of the disease and less severe forms, but either you are ill or not... What else is there in between?
 
* You are weighting each feature equally. For instance PAM1, PAM25, and BLOSUM62 are treated equally. The three secondary structure prediction are of course not independent.
 
* You are weighting each feature equally. For instance PAM1, PAM25, and BLOSUM62 are treated equally. The three secondary structure prediction are of course not independent.
  +
--> but sometimes different. A weighting function would have actually been a good idea, but since we are not done yet, it would have made no sense to develop one.

Revision as of 20:59, 18 June 2012

Praise

  • Nice tables
  • Nice visualizations of the mutated residues. Is this pymol?
  • Plenty of physicochemical properties.

Criticism

  • Does the secondary structure prediction refer to the sequence before or after the mutation?

--> Since we used the files from Task 3 (see Journal), it is from the native structure

  • What are your reasons for taking into account the substitution score of PAM1 and PAM250? Is the evolutionary distance not too short and too far, respectively?

--> We were said to do that

  • I think the substitution scores of the three matrices are not directly comparable. PAM1 should have lower scores than PAM250 relative to the maximum score.

--> We díd compare them relatively not the absolute values

  • What do the entries in the PSSM table mean? It is obviously not the substitution score. In case of P40S: is P(P|40) = 0.81 or P(S|40) = 0.81?
  • You classify the features either as disease causing or not disease causing. But what if a feature is in between?

--> There are more severe forms of the disease and less severe forms, but either you are ill or not... What else is there in between?

  • You are weighting each feature equally. For instance PAM1, PAM25, and BLOSUM62 are treated equally. The three secondary structure prediction are of course not independent.

--> but sometimes different. A weighting function would have actually been a good idea, but since we are not done yet, it would have made no sense to develop one.